Thirteen
by Fifth Horseman
Summary: Misato was determined to find the truth hidden within NERV's walls. One should always be careful what they wish for.
1. Chapter 1

**Disclaimer: **I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

I originally projected that this story would be out in late March or early April. So much for deadlines, I should know better.

Four months since my last submission...I guess times still flies even when you're stressed out and miserable. But enough with the negativity.

Here's my latest, it should be a 2 chapter affair and I'm still working on the second chapter. Usually I won't post multi chaptered work until the whole thing is completed, but I felt the need to get something out. This is one of the ideas for a 'younger Misato' that I've been kicking around for several months and finally got around to writing it.

So, give it a read and leave a review if you please. I hope you like it.

**Thirteen**

**_Chapter One:_**

The silence in the cavernous room went from the mere undisturbed quiet of a long abandoned space, to a suddenly heavy and oppressive thing that seemed unnatural and impossible in its scope. So much so that it affected not only the physical world, but had also temporarily silenced the brief flow of sudden, chaotic thoughts in the mind of Misato Katsuragi. Such was the case when one laid eyes upon something that should not be.

She should never have come back down here again, it had been a bad, bad idea. She never should have returned to the shadowy depths of Terminal Dogma and to the horrible secrets it held. She had been well aware that if she found anything in her searches through the recesses of the base, it would most likely be shocking and unpleasant. But she hadn't expected anything like this. She hadn't expected to find something that would shake her very soul to its core.

The room she currently stood in was a lab, very similar to the one where she and Shinji were shown the clones of Rei Ayanami, but with at least two dozen large, upright, glass containment vessels rather than a large tank. The sight of those giggling, soulless, beings disintegrating before her in that tank still gave her nightmares.

Still, it hadn't been enough to suppress her now all consuming quest for answers, and it had pushed her once again into the little travelled depths of the facility to seek out the unknown truths hidden within it. So far the quest to learn NERV's secrets had resulted in Kaji being killed and her Shinji being left in a state of shock and very badly shaken. She still didn't know everything that was going on with NERV, but even so, she had never suspected that things would get so bizarre and horrifying.

The vessel before her, like the rest of them, was situated on a raised platform that took up most of the centre portion of the cavernous room. It was beyond the safety rail she was currently trying to crush in her white knuckled grip, and it was the only one that wasn't empty. As much as she tried to look away from what was inside of it, she couldn't tear her eyes away. The sheer incomprehensible nature of what she was seeing left her transfixed and unable to think.

She covered her mouth with her left hand and swallowed hard, trying to ensure that her meagre lunch didn't make a sudden and unwanted reappearance. Finally letting go of the rail, she took a couple of shaky steps backwards until she bumped up against a large control console, then her legs gave out completely and she slowly sank to the floor.

Her breath began to come in great, heaving gasps and it was all that she could manage to keep herself from hyperventilating. Her body began to shake uncontrollably and tears streamed down her cheeks, her mind threatening to shut down on her completely. There was no way that what she was seeing could possibly be true. It just couldn't, it wasn't possible.

She had already seen a lot of incomprehensible things in her life. Second Impact. Angels. Evangelions. In Terminal Dogma alone she had already seen the skeletal remains of failed Evangelions, a crucified Angel, and the clones of Rei Ayanami. She had thought that nothing could surprise her anymore, that nothing she could ever see or discover in this place could top what she had already seen, or leave her feeling any more horrified and disgusted.

Obviously she had been very wrong about that.

Nothing in particular had drawn her to this specific room, it was just one of the very few whose electronic lock yielded to the doctored ID pass card she had found in Kaji's apartment. The card which had escaped the notice of Section 2 when they ransacked her former lover's living quarters.

She had attempted to gain information by hacking some of the lesser subsystems of the MAGI, she wasn't good enough at it to try cracking the main system, but the effort had turned up nothing more than fragments of files and documents that mentioned various projects, including the elusive Instrumentality Project. However, that's all they were. Fragments. Basically useless bits and pieces that held no explanation as to what any of them were and which gave her very little to work with.

That left her with no other options than to start snooping around and see what she could get into. It was risky and she knew that she could be caught at any time, with the likely outcome being a cell next to her dear friend Ritsuko. Of course it could also get her a bullet in the head, but if that was how they wanted to play it she sure as hell wouldn't go down easy.

At the moment however, all of that was irrelevant. Someone could walk up to her right now, press a gun to her head, and blow her brains all over the room and she would be hard pressed to even notice. Her mind was locked in a loop of unthinkable possibilities and the rest of the world around her had temporarily ceased to exist.

The oppressive silence was shattered into a thousand pieces by her sudden, soul rending scream.

* * *

If humanity were to give out an award for those who were among the most downtrodden and kicked around by life, it could well be named after Shinji Ikari. True, the boy hadn't done very much to help himself avoid such pitiful circumstances, but he also hadn't been given a hell of a lot of help to be anything other than the too often kicked dog that he was.

He had lost his mother at a very early age and was promptly abandoned by his father because the man had no use for him, at least not yet. He was made to feel like he was a burden and an annoyance to the people who where entrusted with his care and education, and he was forced to learn how to fend for himself very early on in his young life.

No one had ever taught him how to stand up for himself, or spent enough time with him to allow him to grow comfortable in the presence of others, to learn how to interact with other people without being paralyzed by nervousness and fear. No one taught him that rejection and pain were just as much a part of life as acceptance and pleasure, and that he deserved love and happiness just as much as anyone else did.

The skinny, physically unimposing boy became so withdrawn that to be anymore so would have seen him disappear from existence entirely. Something which at times he had found himself wishing for very much.

Even if he had arrived in Tokyo 3 well adjusted and happy, he was sure that the last year would still have beaten him down. Fighting the Angels terrified him. For that matter, so did Unit 01 and it didn't help that he was very confused as to why, despite that fear, that he often felt safe and even a little at ease when inside the beast. Not to mention that the number of times he had awakened to find himself in the hospital hadn't exactly done much to ease his frayed nerves and boost his confidence either.

Even amidst the fear and uncertainty he had made some friends, and at least for a little while he felt like his life might have been changing direction and something good may yet come out of it all. Typically though, as was usually the case when he got his hopes up about something, it all went downhill and turned to shit.

He had nearly killed Touji and now he and Kensuke and Hikari were all in Tokyo 2. In Misato he had met someone who truly seemed to care about him, but for several weeks now he had seen less and less of her and even when they were in the same room together, little was said between them.

Rei was someone he had wanted to get to know better, but ever since he had found out that she was a clone he had been unable to go near her. This Rei wasn't the one he knew. This wasn't the Rei who had protected him, smiled for him, and gave her life to protect him. _It_ was an impostor wearing her face.

Asuka. He didn't quite know how to quantify his relationship with the mercurial redhead. He liked her and wanted to be her friend, but she treated him like garbage most of the time. He admired her spirit, but he hated her attitude. One minute he was mesmerized by her, the next he wanted to kick her ass. Now she was laying motionless in a hospital bed, locked away within her own mind. No one knew if she would ever come out of it.

Then there was Kaworu. He had seemed to understand his pain. He wanted to be his friend and expected nothing in return and Shinji was glad to be his friend. He wanted him to be happy, but he destroyed all potential for that happiness when he revealed himself to be an Angel. When he forced Shinji to kill him, it nearly destroyed the already troubled boy.

Since then, Shinji had kept himself busy with two main activities. Laying in the dark of his room, trying to drown his mind in the music playing on his SDAT, or wandering around aimlessly in the ruins of Tokyo 3 or the less travelled regions of NERV headquarters.

He had found that he could wander for hours with his mind becoming a virtual blank, a blissful and welcome relief from the turmoil usually contained within it. The pain and the pressure seemed to disappear, or were at least pushed so far to the outer reaches of his consciousness that he couldn't feel it anymore.

It was almost as if he went into a trance, something like a state of not quite awareness. It was a solitude that he couldn't find anywhere else. He supposed he was on dangerous ground and ran the risk of ending up like Asuka, but he really didn't care anymore. All he knew was that when he wandered, he didn't feel the pain. He didn't slip back into the waking world unless something caught his attention or he became tired and would then go home and sleep peacefully for a few hours before the pain and turmoil crowded his mind once again.

He had been wandering around the labyrinth of corridors beneath NERV headquarters when he found himself rudely brought out of his blissful stupor. He had come to _that_ place again, the room that had once held Rei's clones. He didn't know why he kept ending up there every time he wandered the complex, and he really didn't want to give it much thought.

Like usual, he thought about going inside, he knew the door was no longer locked, but in the end he never ventured in. It was partly because of what he had learned about Rei while in that room, but it was also because seeing her clones disintegrate had been like watching her die again. He still saw those blissfully unaware smiles and heard the giggling laughter in his sleep.

It was doubly hard to deal with because he had really liked Rei and seeing her die in order to protect his worthless hide had been hard enough to deal with, but this…

He shook his head violently in an attempt to dislodge the painful memories from his mind before they replayed themselves again. After regaining a semblance of composure he stumbled off down the corridor and resumed his wandering, desperately hoping that he would soon return to that blissful, zoned out state of mind.

He soon came to the end of the corridor and entered the stairwell to make his way down to the next level. It was a long way between levels, with the stairs criss-crossing back and forth several times as you went down. He could have taken the elevator, but there was less chance of running into someone unexpectedly if he took the stairs.

As he exited onto the next level, he saw Misato entering a door about halfway down the hallway. It wasn't really too much of a shock to see her down here, he knew that she had been up to something for the past few weeks but he wasn't entirely sure what. There had been several nights before he started wandering where he had tried to work up the courage to go and talk to her, to try and break the uneasy silence that had grown between them. However she was always locked away in her room and his resolve would evaporate by the time he got to the door.

Several times he had sat down in the hall next to her door after his failed attempts, disturbed that he couldn't re-establish contact with the one person who had cared about him. He listened to her cry, which only made him feel worse, but he also heard her talking to herself as she hammered away at the keyboard of her computer. He caught enough tidbits to know that she was deeply immersed in trying to find something, but he wasn't sure what it was. Now that he saw her down here he realised that she must be trying to find out what else was hidden in the dark shadows of NERV.

Personally, he had already seen more than enough to last him a couple of lifetimes, that was why he never bothered trying to get into any of the rooms he wandered past. He simply didn't want to know.

He felt his need and desire to talk to her once again crowding his mind. His inability to express his feelings to others meant that he could never tell her how much she really meant to him. She had cared when no one else did. She had known nothing about him, yet she had welcomed him into her home and let him make it his home, something he felt like he had never had before.

True, she was a slob and she drank too much, she was immature, she teased him endlessly, and she paraded around the apartment half naked. But, in the brief moments where he allowed himself to think about it, he realized that he wouldn't have her any other way. He realized that he loved that crazy, troubled, beer soaked woman. She was his guardian and his commanding officer, but she was also just Misato, his friend and quite probably his only lifeline out of this mess his mind and his life had become.

He wasn't stupid, he knew she had problems of her own. Hell, he had come to the conclusion that it was practically a job requirement for NERV employees to be severely messed up in the head. But the weight of their respective troubles had pushed them away from each other, though in his mind he was convinced that he was more to blame for it than she was.

With all of this on his mind, he slowly made his way to the door she had entered, trying to keep up the slim flicker of courage to go and talk to her. He was just stepping across the threshold when he heard her scream.

* * *

Misato was so out of it that she didn't even notice when Gendo Ikari walked up to her, reached into her jacket, and removed her pistol from her shoulder holster. He stepped back, keeping the weapon trained on her.

"It seems that you've found something you're having trouble comprehending, Major Katsuragi," he said to her, finally awakening her from her unresponsive state.

"What the hell is this?!" she rasped, still trying to get her breathing under control.

"It is exactly what you fear that it is," he answered simply. He glanced to his right and smirked. "It is rude to eavesdrop, Third Child. Close the door and come over here and join your guardian. Misery does love company after all."

The summons from his father snapped him out of the terrified paralysis he had fallen into when he heard Misato scream. Reluctantly, he obediently entered the lab, closing the door behind him, and shuffled over to his father. His eyes glanced from Gendo, to the gun, then to Misato. He was alarmed that his father was pointing the weapon at her, and he was equally concerned by the distraught look on her face and followed her gaze to the cause of it.

It took a few moments for his already congested mind to focus on what he was seeing inside the tall glass tank. His eyes went wide and all of the air went out of his lungs as his brain finally processed it and recognition struck him. It seemed like yet another important part of his life was turning out to be something other than what he knew it to be.

He staggered backwards, stopped only by the firm grip of his father's hand on his shoulder. Gendo easily steered him towards the control console and guided him down until he was sitting on the floor next to Misato.

The elder Ikari derived no pleasure from their reactions, but he also felt no remorse either. Remorse and regret were things he had no time for and had cast them away a long time ago. They served no purpose other than to distract one from their goals and he was never one to lose focus. Now, with the moment he had worked so long and so hard for drawing ever closer, he had taken care of two possible distractions.

It hadn't been hard to follow Katsuragi's progress as she snooped through the lower levels. There were many hidden cameras and sensors that even the most well trained observer would be hard pressed to find. When he saw her heading towards this particular level, it was a fortuitous bit of luck that he gladly used to his advantage. He ensured that the door to this lab would yield to her card and he used his private express elevator to arrive before her and entered through a concealed door in the back. It also got him out of the more vulnerable levels of Central Dogma, since the JSSDF had been about to launch their attack on the facility as part of SEELE's Instrumentality plan.

The sole object of interest in the long unused lab had rendered the Major virtually harmless, just as he knew that it would. She was paralyzed at the sight, her entire world shaken and turned on its head, effectively negating any threat she had posed to the consummation of his scenario.

While she had posed a threat and needed to be dealt with, the same couldn't be said of the Third Child. He was a broken and used up commodity and was of no consequence. While it mattered very little as to his whereabouts leading up to the culmination of events, it was just as well that his aimless wandering had brought him here. At least he could spend the last dying moments of humanity with someone who actually cared for him.

As for Shinji himself, he felt like someone had wrapped their hand around his heart and had begun to squeeze. Tears were streaming from his eyes as he looked to Misato. She was trembling and silently crying as she just stared lifelessly at the sight before them. He didn't want to look at it again. He didn't want to acknowledge that what he was seeing was real. Somehow though, he felt compelled to look. Not looking wouldn't make it any less real, or confusing, or frightening.

He wanted to run away. Oh god, how he wanted to get up and run away as fast and as far as his legs would carry him. But he knew that he couldn't. The sight of Misato being so broken somehow held him in place. Even the fact that his father was watching over them with a gun pointed in their direction seemed somehow secondary to that. Misato didn't break, that was one thing he had been sure of if nothing else. Even after she found out about Kaji's death, she hadn't broken. She had bent, she had cried and she had grieved, but she got back up and kept going. He was afraid that there wasn't any getting back up this time.

He turned his reluctant gaze back to the subject of their attention, swallowing hard and trying not to come apart at the seams. The tank was filled with a liquid that made him think it was LCL, but it was a lighter shade than normal and he could feel a definite, sharp chill coming off of the vessel. Various tubes and wires snaked through the liquid from above like high tech tentacles, and were attached to a naked human figure floating weightlessly in the centre of the container.

The figure was female and if Shinji had to hazard a guess he would have said she was at least the same age as he was. She was very pretty, with dark hair sweeping down below her shoulders, but it was hard to tell exactly what colour it was through the tint of the fluid. Under other circumstances he would have blushed furiously at seeing the girl's slim body and generous breasts, maybe even launching into nosebleed territory. In actuality, the sight wasn't totally unfamiliar to him, since he had seen it before, along with the long scar that cut across the girl's abdomen. He had just seen an older version of her was all.

"Third Child, meet the real Misato Katsuragi," Gendo said dispassionately to his son. "The woman sitting beside you is a clone of this girl, number thirteen to be exact. She is the culmination of the research that eventually led to the creation of Rei Ayanami and the foundations of the dummy plug system."

"No!" Misato croaked. "It's not true! You're lying!"

"The truth is floating right in front of you Major," he said calmly. "And it is indisputable. Your unwillingness to accept it, does not make it any less so."

With great effort, she managed to regain a small measure of control. "Why?" she asked, her voice unsteady and full of bitterness. "Tell me why."

"It was a matter of convenience," he answered. "We had a need and she," he gestured to the tank, "was an available test subject."

"Just another Second Impact orphan," she seethed. "No family left, no one to miss me. And being in a near catatonic state and unable to speak, I couldn't object."

"Precisely," the Commander agreed. "Despite the illegalities of it, mankind had nevertheless pursued the ability to clone a human being and had successfully done so before Second Impact. SEELE, and NERV's forerunner Gehirn pioneered much of the process, with an eye towards using clones to pilot the Evangelions, either as live pilots or as living remote control units."

"The dummy plug system," she spat in disgust.

"Indeed," he confirmed. "One of the initial problems however, was that we could not wait for the clones to grow to maturity by natural means. We needed the program to be as close to functional as possible before the expected arrival of the Angels."

"You needed to accelerate the growth rate of the clones," Misato guessed logically, her anger helping her focus and start regaining her composure.

"Correct," Gendo affirmed. "Our genetic biologists were the best in their field and they had a workable method that had already yielded promising results in test animals. The problem was in applying that same procedure to a human body. It took another two years and eight attempts before they were able to perfect the accelerated growth of a human clone."

"But clones don't have a soul," Misato said, shivering as she remembered what Ritsuko had shown and told them. "Rei's clones…"

"Were little more than animated dolls," Gendo finished dispassionately. "Spare parts that on their own were useless. The lessons that were learned through your predecessors also allowed our scientists to work out the final problems in acquiring a soul from a living being and implanting it into a soulless body. It also gave excellent results in the transference of intact memories from one clone to it's replacement, or the burying of selected memories so deeply into the mind that they might never resurface."

"That's why Rei didn't remember anything," Shinji mumbled.

"So how much of my memory did you bury?" Misato asked accusingly, her fire now beginning to return to her.

"All your memories of visits by medical personnel associated with the project were suppressed," Gendo answered. "As were all memories pertaining to any location outside of the mental hospital you were admitted to after Second Impact, up until the time you were released."

"Why didn't you just put my soul back into its original body?" she asked accusingly. "Why not just erase all of my memories from Second Impact on and send me off to an orphanage somewhere, where I would be out of sight and out of mind?"

"There were three main reasons," the Commander began. "The first being the remote and unacceptable possibility that the memories would resurface, which coincided with the second reason. Your whole life from that point on was a case study to gauge the long term effects of the process. You have been under constant observation ever since."

"And what was the third reason?" she asked, her voice taking on a cold, hard edge.

"The third reason is the most important." He very nearly smiled. "It was because I had a use for you. I used your desire for revenge against the Angels to turn you into what you became. A skilled tactical commander who would willingly and repeatedly send children into battle, no matter how much it hurt them or how much it hurt you to do so. You performed your duties beyond all expectations, Number Thirteen."

"You bastard!" she screamed, lurching to her feet in order to attack him. She didn't get far. He fired her confiscated pistol, the round slamming into her left shoulder and sending her crashing against the guardrail and sliding to the floor in a world of searing pain.

"The end is coming soon enough Major," he told her, his voice still calm and emotionless. "Do not hasten your end anymore than is necessary."

Shinji was frozen in place, unable to move. The sound of the gunshot had made him jump, but he was too overwhelmed by everything his father had just told them to move on his own. Even as the woman he cared so much about writhed in agony on the cold cement, he could do little more than stare at her in disbelief.

She was a clone. Number Thirteen. The words kept echoing across his mind like some horrific recording that was caught in a loop and he couldn't make it stop. Finding out about Rei had been like a shot to the gut, but this was a hammer blow to his heart. The rational part of his brain told him that it didn't matter. She may be a clone, but she was still the Misato he had always known. She hadn't changed. She hadn't had her soul put into another copy of herself and her memories hadn't been suppressed. She was still the same.

But the not so rational part of his mind was in panic mode and on the verge of overload. He had seen, heard, and experienced far too much. Evangelions. Angels. Clones. Murder. Betrayal. Death. The crushing responsibility of saving humanity sitting upon his small shoulders. None of these were things that a fourteen year old should ever have to worry about.

He lowered his head into his trembling hands, his fingers digging into his scalp as if they were trying to worm their way through his skull and into his brain. His heart was pounding in his chest like a jackhammer and his breath was coming in short, shuddering gasps. Hot tears rolled down his face, and he wanted to scream, but his voice wouldn't work. The last anchor holding him in place was gone and he just wanted to curl up into a ball and disappear.

His breakdown was interrupted and put on hold by a horrendous, thundering boom that made the entire base shake, even this far down. It felt and sounded like the world was coming to an end.

"It seems they're getting impatient," Gendo muttered before turning his attention back to his audience. The time was almost at hand. "Both of you have played out your assigned roles and are no longer necessary," he calmly informed them. "In a manner of minutes all life on this world will end and mankind's suffering will end with it. I will finally be reunited with my Yui."

"What are you talking about?" Misato's pain ragged voice rasped as she tried to pull herself up into a sitting position.

"I am talking about Third Impact, Number Thirteen," he answered, the words chilling her to the bone. "The end of all life on this miserable world, brought about and directed by human hands, not Angels. The ultimate goal of our entire battle to defeat the Children of Adam. I will enact _my_ version of SEELE's Instrumentality Project. There is nothing that you or anyone else can do to stop it now."

His words were his last cruel act, spoken for no other reason than to let her know that she had failed to uncover the truth she had so desperately sought. And he had no intention of explaining to them what the end entailed. He had neither the time nor the inclination to do so.

"You both performed the roles I set for you quite well," he added as he turned and began walking to the hidden exit in the back of the lab, his voice fading in the distance. "This moment could not have arrived otherwise."

"I'm so fucking glad I could help!" Misato spat. The only response she got was the sound of a door opening and closing and a heavy lock bolt sliding into place.

She reached up and grabbed the top of the safety rail and finished pulling herself upright. She leaned her head back against the cold steel and fought off a wave of pain and nausea. Silent tears began to roll down her face once again.

Her mind was filled with confusion and chaos as long suppressed memories began to flash in and out of clarity. She had glimpses of a containment vessel like the one her true self currently floated in, only the view was from the inside looking out. There were white coated scientists taking notes and working at computers. She could remember the feel of the tubes that fed her body and carried away waste, and the electronic leads that had been attached to her head and various other parts of her body to monitor her progress.

The strange thing was that there was no emotional attachment to these recollections, they were just 'there', but she soon realized that they must be latent memories from events that had happened before her current body received the soul.

'_Number Thirteen,'_ she thought bitterly. _'I'm nothing but a number, a tool.'_

She tightly squeezed her eyes shut and tried to push the memories away, but they were stubborn and didn't want to go. She forced her injured left arm to move, the searing pain from the gunshot wound flaring anew and burning the unwanted memories out of her conscious mind. She bit her lip until it bled, trying to keep herself from voicing the pain she was in. As it began to ebb, she worked at catching her breath and settling her mind.

What she was, was different from who she was, and who she was hadn't changed with the knowledge that she was a clone. She was still Misato Katsuragi, survivor of Second Impact, Director of Operations for NERV, and guardian of Asuka Langley Sohryu and Shinji Ikari. Despite the mind numbing revelation she had just experienced about herself, she could not lose sight of that. She was who she was, and she had to hang onto that for not just her own sanity, but for that of the broken young man sitting across from her.

Shinji really didn't know what to do, so he did what was always so disturbingly natural for him. He did nothing, and nearly suffocated on his shame because of it. How could he be so weak? Successful or not, Misato had always tried to be there for him and there she sat, devastated and in pain for the second time in the last few weeks and he couldn't even do as little as speak to her. Even if he could, what would he say? What do you say to someone who just had their life turned inside out? How do you offer them comfort when they were just hit with something so unbelievable?

Besides that, there was the truth that his father had been working towards Third Impact all along. All they had been doing was fighting for who got to initiate and control the end of the world. He was the son of a man who wanted to destroy humankind and he was ashamed of that association. It left him with a rather sick and disgusted feeling.

"So I'm a lab experiment huh?" she mused tiredly, breaking the silence as she glanced over her shoulder to regard the inert form in the tank. "I suppose I could take the easy way out and blame all of my bad behaviour on that."

The attempt at humour did nothing to lessen the flow of tears still silently trailing down both of their faces. The truth was, at this point she didn't really know whether to laugh or cry at the farce her life had turned out to be. At least it wouldn't last much longer, and for Shinji's sake she could bluff for that long.

"Shinji," she called out, her voice as gentle as she could make it. His gaze remained glued to the floor in between them. "Look at me Shinji…please."

Slowly, his head came up and his eyes eventually met hers, though they had a lost and empty look in them. He looked so scared and so alone, like he had nothing left in the world.

"I'm still me Shinji," she told him with as much reassurance as she could, though she wasn't sure if she really believed it herself. "I'm still the same Misato you know, I'm just not the one I thought I was."

His eyes seemed to finally come into focus. "It was all for nothing," he said quietly. "All of the pain. Touji, Kaworu, Asuka and Rei…all that we've been through was for nothing."

"Depends what side you look at it from," she sighed. "And from where we're sitting, yeah, it seems like it was all pretty pointless. Beat the angels or not, we lose either way, but I guess none of us really had any choice."

"I've been thinking a lot lately that I wouldn't mind dying," he admitted to her, his voice shaky. "Sometimes I even felt like I deserved it. I thought that it would be alright because it wouldn't hurt anymore. But now that I know it's coming…I don't know."

"I'm not ready to die," she responded, a hint of defiance in her voice. "And I don't want to either. Okay, I'm a clone. I can't do anything about that. And I don't know now if my motivations were my own or if everything I've done for the last fourteen years were things that I was conditioned to do or to believe. In any case, I've made a ton of mistakes and done a hell of a lot of things that I regret."

She used the safety rail to pull herself up to her feet. Loss of blood was making her a little woozy and she wasn't very steady, but she was determined.

"But in spite of all of that, it was still my life and I lived it. I'm not giving it up that easy. I'm not gonna sit here on my ass and cry about it and wait for death to come and find me. If it wants me, it can come and get me while I'm on my feet and looking for that bearded bastard with the tacky orange glasses."

Shinji admired Misato's spirit, he always had. She had just been told that she was a clone and that the world was about to end, revelations that were crushing what little life was left in him, but she wasn't going to give up and quietly accept it. She wanted to go down fighting and he wished he had it in him to do the same.

"So whaddaya say Shinji?" she asked him, a small smile finally gracing her lips. "You with me?"

"I…I don't think I can," he stuttered, his voice barely audible. "I…

"Then you're not my Shinji," she said flatly.

"W-What?" Her words had caught him completely off guard.

"My Shinji always kept fighting even though it hurt him and he was scared. He knew it was the right thing to do and he fought to protect the people he cared about."

"I'm not that strong Misato, I'm weak and I'm a coward…."

"Bullshit!" she barked more sharply than she intended, making him flinch. She softened her voice. "You are not a coward Shinji, and you never were. You did what needed to be done because you were the only one who could. Believe me, if I could have piloted the Eva and saved you all of this pain, I would have, and I've wished a hundred times that I could have. Give yourself a little credit, you're a lot braver and a lot stronger than you think you are."

"I wish I could believe that," he said, finally raising his head to look at her.

She looked into his watery blue eyes. "You should believe it, because it's the truth. I've always felt that way Shinji," she admitted.

"You have?"

She nodded. "I just wish I'd said it before. I know I've been a poor guardian. I'm immature, a lazy slob, and I drink too much. I wasn't there for you when you needed me and you certainly took much better care of me than I ever did of you and I'm sorry for that. You made my apartment seem like a real home and you chased away some of the loneliness. And I used you to get my revenge, which makes me a pretty rotten person. But, despite all of my faults, you've stayed with me. You're the only one who hasn't left me or said you hated me."

He sniffled, his tears finally starting to subside. "I could never say that to you Misato. You're the only person who's cared about me since my Mom died. You're not rotten and I could never hate you and I wouldn't leave you."

She reached out and smoothed his ruffled hair. "Thank you Shinji," she said sincerely. "You know, I wanted so much to help you come out of that shell you live in and be more confident about yourself and have a little fun, like a boy your age should." She gave him one of her mischievously evil smiles and winked at him. "Heck, it's too bad I wasn't your age, we could have had lots of fun together."

"M-Misato!" he squeaked as his cheeks turned red.

Smile still in place, she offered him her hand. "So how about it Shinji? This is the last chance you'll have to show the world who you are and what you're made of. Leave all of your pain and self hatred here and walk out of this life with me, with your head up and a smile on your face."

Her desire to live in spite of the knowledge that their lives would soon be over was a powerful thing and it seemed to take hold of him. Despite all of the pain and loss and loneliness that had made up so much of his life, and despite knowing that their lives were about to come to an end, he found that, for once, he didn't feel like he wanted to run away. It was a very odd feeling for him, yet very satisfying. Besides, he could think of much worse ways to leave this life than to be walking hand in hand with Misato Katsuragi.

He wiped away his tears and took her shaking right hand in his trembling left and got to his feet. As they turned and began to slowly walk towards the door, she intertwined her fingers with his and gave his hand a gentle squeeze.

"I don't know if there's an afterlife Shinji," she began. "But if there is I hope we get to go there together."

"Me too," he agreed.

They were silent again for a moment before she spoke up once more. "You know, it's too bad that I didn't know about being a clone long before this."

"Why?" he asked, a bit puzzled.

"Well, if I had known that this body was only fourteen years old I would have jumped your bones long ago."

His face turned red enough to practically light up the room. "…M-Misato!"

"What? Technically it would have been legal…I think."

While he was rendered speechless as his already overworked brain processed this, she bent down and planted a brief, but heartfelt kiss on his lips.

"Just a little something to remember me by."

They suddenly felt a tingling sensation that made the hairs stand up on the backs of their necks, and they both felt as if there was a powerful presence in the room with them.

She squeezed his hand again as they resumed walking. It took a great deal of effort to keep the fearful waver out of her voice. "Don't look back Shinji. Keep going forward."

"O-okay," he said as he squeezed her hand back.

Behind them, an apparition of Rei Ayanami displayed the briefest of genuine smiles before fulfilling her duty. There was a barely audible pop and a splash as their bodies turned to LCL and hit the floor, becoming one amongst a pile of empty clothes. The apparition turned to the containment tank and performed the same duty for the body residing within before promptly disappearing.

* * *

**A/N:** I hope you liked this and I am looking forward to your comments. Your reviews and PM's could go a long way towards the developement of Chapter 2.

I have some work done on it, but that doesn't mean what I have will be what see's the light of day in the end. It could be fluff, or there could be something else entirely. I need to brainstorm it a little more an develop a list of possibilities to choose and work from.

No matter how it turns out, or what it turns out to be, it will get done. I will never leave a story incomplete or leave it hanging.

And since you're hanging around here, why not check out my other work. You know how to find it.


	2. Chapter 2

**Disclaimer: **I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

Originally I thought this would just be a two chapter story, but it stretched itself into three.

So, here's Chapter 2, I hope you enjoy it.

**Thirteen**

_**Chapter 2:**_

Shinji squinted his eyes against the glare of the sun as he awoke and struggled to sit up. He was exhausted and his head was filled with an ache that could only be described as feeling like it was heavily overstuffed with wet cotton balls. His mind had been forced to assimilate so much that it was a wonder he hadn't gone insane from the overload.

"Ugh," was his appropriate commentary as he massaged his temples and took a few deep breaths. He froze for a moment when he suddenly realized that he was naked.

'_Why is this not a surprise?'_ he thought.

Before him, the gigantic head of the Rei/Lilith entity was slowly dissolving into the red-orange liquid of the LCL sea, and was surrounded by the petrified remains of SEELE's mass production Evangelions. It was a disturbing sight that sent a shiver up his spine and only added to the fear and uncertainty he was feeling.

Even so, despite the disturbing nature of the view and with the only sound being the gentle lapping of the LCL against the shore, it was kind of peaceful. In an eerie, disturbing, apocalyptic sort of way.

"You deserve better than this Rei," he whispered. "You deserve a chance to live for yourself."

During Instrumentality she had guided him through a replay of what had been his life, showing him all of the things that he blamed himself for and showing him why they weren't his fault. She also showed him the things that were, and why they were. She was brutally honest with him. He had to be exposed to the cold, unvarnished truth if he was to make the decision she was going to leave in his hands. He needed to know if he was ever to have a chance for a better life if he chose to keep living. She thought he deserved no less.

At first he had been very angry with himself and it had all left him feeling rather foolish and humiliated. He felt like he had been on the wrong end of a bad joke for a very long time and everyone else had been in on it. When he was given the choice to decide the fate of mankind he had been ready to flush it down the cosmic toilet at first, but Rei had made him calm down and see things with a greater degree of clarity.

Of course, that was no easy thing when you were naked and flat on your back in a strange, red tinged world, with an equally naked Rei quite literally joined into one being with you, and at the hips no less. All while essentially being at the end of your mental rope. Even so, she helped him to see a great many things so clearly and helped him to understand the nature of his life and human life in general. She saved his sanity, and quite likely his soul as well.

In the end he decided to reject Instrumentality. He realized that it was better to remain as individuals and have both pain and happiness in life, each being necessary to define the other, than for all to be one entity that had no awareness of anything at all.

He knew deep down that it was the right decision, but he was very scared and he knew that his life would not suddenly become wonderful and joyous. He had been through far too much, lived with too much stress and strain on his mind and his soul for that to ever happen. He knew that he would struggle until he could get his legs under him and be able to stand on his own, something he had never been able to do before.

The first test came when he saw his mother just before he came back. He had missed her so much and seeing her again was almost more than he could handle. She told him that she loved him and was proud of him, that he had made the right choice and that everything would be alright. She told him that he had a bright future ahead of him and that all he had to do was grab onto it and make it his. It hurt badly that she wouldn't be going back with him, but at least this time when they parted ways he got to say goodbye and tell her how much he loved her.

"I promise Mom, I'm going to really try and live this time," he vowed to the blood sea. "I know it won't be easy but I'm going to try my hardest to make it work."

In truth, anything less was not an option and he knew it.

He yawned mightily and vigorously shook his head in an effort to try and stay awake. He was so tired, completely spent both physically and mentally, and he could think of little else but laying back down and letting sleep overtake him. At least until he caught sight of something out of the corner of his eye that is.

It was a naked foot.

He froze, not sure if he really wanted to turn and see who had came back with him. Rei had said that anyone who wished to return could do so, but he really wasn't ready for company right now. He really just wanted some time to sort himself out and pull himself together before having to deal with anyone else.

'_Agghh, for crying out loud, stop being so pathetic!'_ he mentally derided himself. _'Just calm down and go see who it is. Besides, they might need help.'_

Steeling his resolve, but unable to quell his nervousness, he turned and looked back to his left, his eyes going wide and his mouth hanging open at the sight before him. There, slightly behind him and just as naked as he was, was the girl from the containment tank. He found himself staring at her for a long moment before his brain re-engaged itself.

"Gah!" he yelped as he quickly turned away, breaking into a full body blush. He was definitely awake now.

'_Naked on a beach, with Misato's original body, which is also naked.' _Panic threatened to overtake his brain. _'What the hell do I do now?'_

The first thing he did was to take a deep breath and try to calm down, since panicking wasn't going to get him anywhere. Besides, after living with Misato for a year and his recent experience with Instrumentality, a little nudity shouldn't be much of an issue for him. But, he was still Shinji Ikari after all…

"_Does this mean that her soul got put back into her real body?' _he hoped so, because life just wouldn't be the same without her around. He also remembered all too well the vacant eyes of Rei's soulless clones and he never wanted to see something like that again. Unfortunately his line of thinking only made him more nervous. If he saw that same vacant expression in her eyes he was sure he would go mad.

"But I have to make sure she's alright," he told himself. He could always wait until she awoke on her own, but he had no idea how long that could take and he would only become more of a nervous wreck the longer he waited.

Taking a deep breath, he got up and cautiously approached her, shielding his…parts…with his hands. She didn't need to wake up after this ordeal and be confronted with his male accessories and he didn't really want them to be seen. Especially not in their current state.

'_Oh why now dammit!' _He sighed. _"Asuka was right, I must be a pervert.'_

As he knelt down next to her, not too close, he noticed a few things that weren't obvious on his initial look. First, she was wearing the cross that adult Misato had always worn. Second, she had several round, red marks on her body. After a moment of puzzling on it, he realised that each spot corresponded with where a tube had been attached to her body while she was in the tank. Each spot had the look of a wound that was in the final stages of healing and disappearing entirely.

He glanced at her abdomen and was surprised to see that the once jagged, ugly, fish-belly white patch of skin that marked her like a brand, now looked like the other healing wounds. He could tell by the slight difference in colouration around its edges that it had gotten smaller.

'_That should make her happy,'_ he thought, knowing how she felt about the scar.

While some would have taken advantage of the situation by taking a good look at what lay before them, or worse yet, getting hands on about it, Shinji did not. He was having a tough enough time already. It wasn't just his usual fear of seeing and being near a naked girl, but also his respectful nature. So while others may have let their eyes or hands wander to places they shouldn't, he was content to simply look at her face.

She looked peaceful lying there, with her long purple locks spread out around her head and her bangs ruffling in the gentle breeze that had kicked up. Her face looked so relaxed and untroubled, unlike any other time he had ever observed her in sleep. His eyes were drawn to her lips which were slightly parted and he felt himself becoming somewhat mesmerized.

"She's so pretty," he whispered aloud, his fatigued mind not realizing what he had just said.

She began to stir and let out a low groan, like one would expect from someone who was just waking up, but wasn't looking forward to it.

"But I don't wanna get up," she muttered, her voice sounding rough and strained.

He couldn't help but laugh, which made her eyelids flutter open.

"Sh…Shinji?" she rasped.

"Eep!" he squeaked as he turned away a little, trying to better conceal himself. "I'm right here Misato," he answered.

"So that was Instrumentality huh?" she said thickly as she struggled to lift her head and look around. "You went to an awful lot of trouble just to get me naked on the beach didn't you?"

Shinji's brain locked up like it was running on an old version of Windows and he uttered something that sounded like 'urggkh' , before toppling back onto the sand. Of all the things he thought she might say when she woke up, that wasn't one of them. Though, he supposed he should have expected it.

"And it looks like you're _really_ happy to see me too," she added. She just couldn't resist.

Horrified, he quickly rolled away from her to hide the offending appendage. "I'm sorry," he apologised, his brain obviously having rebooted into default mode.

"That'll be enough of that," she scolded. "If you hadn't had that reaction, I'd have really been worried about you. And a little offended too."

He groaned and pounded his head against the sand a couple of times. _'Everything we just went through and she's teasing me already just like nothing happened.'_

"Hey!" she exclaimed. "What the hell…my boobs got smaller!"

"Your whole body got smaller Misato," he told her, a hint of exasperation in his voice. "You're back in your original body."

"Unhhh," she groaned, causing him to turn and look at her. She was trying hard to sit up. "Damn it's hard to move. Give me a hand here would you Shinji?" She could see the reluctance on his face about approaching her in their unclothed state. "Please?" she asked softly, looking him in the eye. "It's okay, and I won't tease you anymore."

Trying his best to keep his man parts concealed, he made his way over to her.

"I can't sit up by myself. I'm actually surprised I can move as much as I am since this body hasn't moved on it's own in fifteen years."

He shakily placed his hands under her shoulder blades and helped her to sit upright. He then had to grab her shoulders to steady her and keep her from toppling over.

"Thanks Shinji." With her limited mobility, she began to give herself a quick once over. "What's with these red blotches?" she wondered.

"That's where the tubes were stuck in your body," he explained. "They're almost completely healed." He hesitated for a moment be fore quietly telling her, "Even your scar looks like it's healing."

She froze for a moment. She knew she wouldn't be able to see all of it without a mirror since it was high enough up her abdomen that her sizeable breasts would conceal it from view. But, she should be able to see the bottom third of her ugly reminder of Second Impact.

She took a deep breath and looked down, seeing what he had noticed earlier. The scar looked more like a shrinking, fading wound, than the patch of deadened flesh that it been.

She took in a shuddering breath. "Wow…it's been a part of me for so long…" Her voice trailed off and she looked out into the LCL sea and to the slowly disappearing entity. "Thank you Rei, or Lilith, or whoever you are now. And thank you Shinji."

"For what?" he asked.

"For choosing to live. You've given us both another chance to live and to be happy." She smiled at him "This may not be the afterlife, but at least we're here together."

_**Tokyo 2, Two Years Later:**_

Shinji slapped his hand down on the alarm clock, killing it's infernal racket. He yawned loudly and rubbed his face with both hands.

"Another restless night," he sighed irritably. "I hope things finally get back to normal after today because I can't take much more of this."

'Today', was the second anniversary of Third Impact. Over the last month he had been pestered by members of a committee responsible for unveiling a memorial in the city's central park. They wanted him to be part of the dedication ceremony and they seemed to have a great deal of trouble with the word no.

There had been no ceremony for the first anniversary, people were too busy trying to survive and restore order, but some people were determined to make a big deal this time around. He would be there, as would every other school kid in the city, but he refused to be put on display as part of it. He was still pulling himself together and the importance of this day in his life was going to be hard enough to deal with as it was. He didn't need any extra pressure, but others were determined to make sure he had it.

Most nights for the last month he had been having dreams about fighting the Angels. Last night, and for the third time this week alone, he had dreamt about his time in the LCL sea and his awakening on the beach. Instrumentality may have changed his life and pointed him in the right direction, but he didn't feel any great need to be reliving it so often.

He knew he wasn't the only one affected by the meaning of this day, it was hitting everyone, but it was particularly hard on those who had been in the middle of the fight and who had suffered the most.

Misato had been acting weird for a few weeks now, definitely not her usual playful self, and he knew it wasn't just because of the upcoming anniversary. Things had become a bit awkward and strained between them and he couldn't seem to find the words or the courage to talk to her about it. Then this whole mess about the memorial came up, bringing its own set of problems.

Otherwise, they had been doing alright, but it was Asuka who was probably in the worst shape of any of them. Her recovery was slow, but she was getting there and she was finally learning to accept the help of her friends. Still, she was refusing to go to the ceremony and he couldn't say that he blamed her. She wasn't ready for something like this and he wasn't entirely sure that he was either.

With a groan he rolled out of bed and shuffled off to the bathroom for a quick shower, which made him feel a little bit wider awake. He put on his school uniform and after putting the kettle on for his usual morning tea, he walked across the apartment and opened the curtains that concealed the balcony door.

The apartment was small, but it was nice, and was situated on the third floor of a three storey student residence building. Across a small courtyard was an identical building that housed the girl's residence where Misato had her apartment, also on the third floor. The occupants of both buildings went to the nearby high school and most of them were on their own, their families still out there in the LCL sea.

He knew he shouldn't, but he felt a little bit guilty about it. Though the decision to come back was up to each individual, he was the one who had been given the choice to make it that way. He knew what it was like to lose his family and he didn't wish it on anyone.

He stepped out onto the balcony and took a deep breath. The early morning air was still cool, but he could tell it was going to be another hot day. He looked across to the other building and saw that the curtains were still closed at Misato's. He smirked. If they weren't open by the time he finished breakfast he would likely have to call her and wake her up again.

'_Then again, I don't think she's been sleeping any better than I have,'_ he thought. He smiled. "At least we're still together and, current troubles aside, we can still count on each other," he said aloud. "Neither of us would be here without the other."

The second test of his new shot at life had been in looking after Misato. With her body in stasis for nearly fifteen years, the nerves hadn't fired and the muscles hadn't moved. Initially, she could barely move and couldn't take care of herself. He helped her work her arms and legs to regain her strength and mobility, and through his fear and nervousness, not to mention embarrassment, he helped her look after her more private needs until she was able to move well enough on her own. It was something that still left him red faced even now if he thought too much about it.

It had been up to him to forage for food, water and clothes, and fortunately he was able to keep them reasonably well supplied. He did his best to outfit their shelter so that it was comfortable and safe, at least as much as a barely habitable corner of a partially destroyed house could be.

They spent a lot of time talking, finding things out about each other that they hadn't previously known, and those talks kept them sane. They needed someone to share their thoughts and feelings with and it helped them so much to do so. One could only keep their pain to themselves for so long and they trusted each other enough to share it. They didn't judge one another, they just listened and comforted each other when it was needed, as well as kicking each other in the ass when it was needed too.

As more people came back, things began to get rough, with fights over food, water, and other supplies. Though he had little real skill or desire for fighting, he made sure that they always had what they needed, and that no one stole what they had or got near Misato. He was successful, but he paid a price for it and had the scars to prove it. He wasn't proud of it, but necessity made one do whatever was required in order to survive, and he had proven that Unit 01 wasn't the only one who could go berserk when things got tight.

Once order began to be restored, they quickly sought help and got out of their crumbling shelter. She was still weak, but doing okay. He on the other hand had a couple of broken bones that needed to be properly reset and a couple of other wounds had become infected. Not to mention that they were both malnourished.

Of course, they were questioned extensively by UN investigators and they cooperated fully, though there were a few things that couldn't be verified until the MAGI's records were examined and they were held at a UN compound until then. It wasn't bad though, they were well looked after and got good psychological and medical care, and with little else to do, he got to catch up on his education. Besides missing a lot due to his duties as a pilot, the quality of what had been taught during that time wasn't very good.

While she didn't need to, Misato had decided to join him. She wanted to go to high school with him when they were finally released. She had never had that experience since, in her previous life, the rest of her education before entering college had been handled by tutors as she recovered from the trauma induced by Second Impact.

It was during their stay at the UN base that they discovered that Touji, Kensuke, Hikari, and Asuka had all came back as well. Due to an administrative error, they had all been put into the same remedial class together while waiting for accommodations in Tokyo 2 to become available.

It was a rather uncomfortable situation for the UN, since they wanted to keep the news of illegal cloning from becoming public knowledge, especially since they had supplied so much of the funding to the organizations that had done it. And, they had no other way of explaining how the formerly twenty nine year old Misato was now a teenaged girl.

Misato herself provided a solution. Tell them the truth, but make them sign secrecy agreements. In exchange for those agreements, the UN would pay for _all_ living expenses for the group and supply full college scholarships. Considering the outcry that would come if the cloning issue came to light, the UN thought it a cheap price to pay.

It had been hard for the others to take, especially for Asuka. She wouldn't believe that the purple haired teen who was practically glued to Shinji really was Misato and she refused to have anything to do with her. It hurt Misato badly and Asuka went into one of her periodic funks that required a few extra visits to her therapist, but she eventually accepted it and began to slowly build a new friendship with her former guardian.

To say the least, he had been shocked when Asuka finally admitted that she really had liked him despite her behaviour towards him. She was a little jealous of how close he and Misato seemed to be, but she didn't want to lose either of them as friends. They were important parts of her life and she had a lot to make up for considering how she had treated them, and she wanted the chance to try.

For him, life now was as normal as it could be and for the most part he was enjoying it. He was just a regular teenager now, going to school and having fun with his friends. There were no Angels or Eva's, no abandoning fathers or uncaring overseers to make his life miserable. It was a life he never thought he could have.

He knew he still had a long way to go yet. He could do without the nightmares and bouts of post traumatic stress, but unlike earlier in his life he was actually trying to live, he wasn't content to just merely exist anymore.

'_Don't look back Shinji. Keep going forward.'_ Those were the words Misato said to him shortly before they were turned to LCL. It became his new mantra and the way he wanted to live. He was trying his best to do it.

As the tea kettle began to whistle he took one last look to Misato's apartment and saw the curtains slide open, followed by the balcony door. A moment later Misato stepped out, dressed in her usual sleeping attire of a pair of his boxers, which she had liberated from his laundry basket, and a short grey tank top. She yawned and stretched her arms above her head causing her short top to rise to a level just short revealing her assets.

He returned the wave she sent in his direction before she went back inside. It was like this every morning, except for the ones where he had to call her to wake her up. It was a little thing, but it was one of those normal, mundane things that made him happy. With a smile, he turned and went to make his tea.

* * *

After waving to Shinji, and ignoring the two dozen drooling gawkers who tried to get a glimpse of her every morning, Misato shuffled back inside. Mornings never had been her thing and it didn't look like that would be changing any time soon. It would be easier though if she could get a decent nights sleep.

"Wark!"

"Aaaah!" she yelped in response. "Geez PenPen, do you have to scare the hell out of me every morning?"

The penguin cocked his head to the side. "Wark?"

"I know, I should be used to it by now. But you always ambush me when I'm half asleep."

"Wark!" With his mission accomplished, PenPen waddled to the kitchen to await his morning fish.

"Mocked by a penguin," she yawned. "Pathetic."

After serving PenPen his fish, she went to the fridge and reached for her morning cold one, popping the tab one handed and quickly guzzling down the contents. She let loose with a loud, lengthy, and very unladylike belch as she tossed the now empty Coke can into the recycling bin. Being back in her real body, she no longer had the physical craving for alcohol, but she still had to fight the mental one. Her morning Coke mimicked and replaced her old behaviour and actually helped her beat down her too slowly fading mental desire to drink herself stupid.

She had actually managed to get her hands on some beer shortly after she moved into the apartment and had started downing them like she used to. It had not been one of her better ideas. She drank until she passed out and was extremely sick the next day. Her true body had never consumed alcohol and the hangover was worse than any she had ever experienced. It also served to wake her up to the fact of just how close to being a raging alcoholic she used to be.

What hurt even more than that realisation, was the look of hurt and disappointment on Shinji's face as he looked after her. She never wanted to see that look on his face again and she sure as hell didn't want to be the cause of it.

After waking up on that beach with Shinji kneeling beside her, and realising that she was back in her original body, she had vowed to change her ways and be the girl she never had the chance to be before. She had an opportunity that most people could only ever wish to have, the chance to relive at least part of her life with the knowledge and experience she had already gained.

She knew it wouldn't be easy, heck, nothing life had thrown at her so far had been easy and she knew that wasn't going to change. But she could change. She had covered herself in filth to spite the memory of her father and to feed her own self loathing. She didn't want to live that way anymore, but sometimes it was hard to stay on top of it. And just lately it had been a real bitch.

She discovered that her memories of her adult life and experiences had changed. To a degree, they no longer felt like things she had done herself, but more like recollections of something she had been told or had read about. It extended to the way she felt in her body as well. She thought she would feel like a twenty nine year old woman inhabiting the body of a teenager, but that wasn't the case. She actually felt more like the way she looked, like a sixteen year old girl.

But while the way she experienced her memories may have changed, the impulses and urges from her past behaviour hadn't. The psychological desire to drink and act out was still there and she had to fight it constantly. Apparently that was one thing the move back to her real body couldn't fix, but she was determined to beat it.

She didn't want to become the woman she had been, but she knew she could never again be the good, well behaved girl she had been before Second Impact ripped her life apart. The real Misato Katsuragi lay somewhere in the middle and she was having a little trouble finding her. She found herself feeling pretty confused and out of sorts at times, and just lately she most certainly hadn't been herself.

She was confused as to her own identity. Was she really the sixteen year old girl she now saw when she looked in the mirror, or was she still the dirty, desperately lonely woman she had been, now just in a shiny new package? She knew which one she wanted to be, but she had been acting too much like her old self and it scared the hell out of her. Today being the second anniversary of Third Impact, and a big reminder of all that had happened, was not helping her situation at all. And then there was that damn memorial ceremony.

Speaking of which, if she didn't stop spacing out and get her shapely little ass in gear she was going to be late. She quickly made and wolfed down a couple of pieces of toast and washed it down with a glass of milk before heading for the bathroom.

She stripped off her night clothes, leaving them wherever they landed, and stepped into the steaming shower where she let the heat seep into her sleep deprived body for a few minutes before lathering up. She stopped for a moment with her hand over the place on her abdomen where the scar used to be. She certainly didn't miss it, but even after all this time she still hadn't quite gotten used to it not being there.

From the standpoint of pure personal vanity, she was very happy that she no longer had to hide it and that alone was a bit of a boost to her self esteem. It was especially nice now when she went to the beach as she no longer had to wear a hated one piece suit. To celebrate that realisation she had went out and bought a very nice red and black bikini. Poor Shinji, his eyeballs had very nearly popped out of his head when he saw her in it, despite all of the times he had seen her wearing less.

For a long time that scar had been a constant reminder of her pain and seeing it in the mirror every day had fuelled her hatred and desire to kill the Angels, no matter the cost. But now the Angels were all gone and fittingly, so was the scar. She raised her hand to her neck and her new motivation in her new life.

She had given her cross to Shinji and replaced it with a silver chain with a pendant depicting the number thirteen. Feeling that against her skin and seeing it in the mirror every morning was a reminder to her to always strive to be something more than that lonely, self destructing, vengeance seeking mess of a woman she had been in her cloned body. She wanted it to be her constant reminder of what had been done to her, what she had been, and what she didn't want to become again.

Shaking off her distracting thoughts again, she rushed through the rest of her shower and hurriedly dressed in her school uniform. She had to admit, she actually looked pretty darn good in the blue skirt and white blouse with blue trim, and, like Asuka, she certainly had enough boys stuffing letters in her locker everyday that agreed with her self assessment.

"Oh crap!" she exclaimed as she looked at the clock. As always, she was running behind. While putting her hair up in a ponytail, because she knew Shinji secretly liked it that way, she rushed through the disaster area that was her apartment and somehow managed to avoid tripping over something before making it to the door and putting on her shoes.

"Damn, I've got to clean this place up before the manager is on my ass again," she groaned. "See ya later PenPen!"

Said penguin waved a flipper in her direction as she dashed out the door.

* * *

Shinji found himself in his usual morning location, standing in front of the apartment complex waiting for Misato. She was never too late, but he was always ready before she was.

He ignored the usual stares and the not quite inaudible comments of, _'How the hell does he get to hang with a babe like Katsuragi?'_, coming from the other students as they passed him by. He heard it even more at school, but like always he just quietly kept to himself and left them to their angst. The fact that he was also often seen around Asuka pissed them off even more and he had to admit that he actually kind of liked it that way.

"One of these days I'm going to get out here before you," Misato told him as she walked up to him.

"I doubt it," he said as he turned to her. Her smile was just as tired as his. "I guess you didn't sleep well either huh?" he asked her as they started walking.

"Not really," she sighed. "Took me forever to get to sleep and I didn't stay asleep for very long."

"I dreamt about Instrumentality again," he told her. "I'm starting to feel almost like I did when I woke up on the beach."

"In that case you're overdressed," she joked, trying to lighten the mood.

"True," he agreed, a small grin coming to his face. They continued on in silence for a few minutes before he spoke again. "It's already been two years."

She nodded. "And things were just becoming nicely normal for us. Then they had to start making a fuss about this memorial. I'm not against there being one, but it's too soon and they shouldn't be trying to pressure you and Asuka into being part of the ceremony."

'_Wouldn't exactly say things have been normal for us lately,'_ he thought. "I agree," he told her. "They called me again yesterday and I told them no again. This time it was some assistant to the UN Secretary General. He still has it in his head to have the pilots on stage when he unveils the monument."

"Bastard shouldn't even be there!" she spat. "SEELE's flunkies were operating right under his nose, pushing their agenda, and he's still pleading ignorance about it when he should just do the right thing and resign." She was almost growling. "If I could still carry my gun, I'd shoot him in the ass."

"Then you'd end up in jail and you know I'd be lost without you around," he said, trying to calm her down.

"No you wouldn't," she countered, sounding all too serious. "You've been carrying my ass since the Impact. You'd be fine without me."

He frowned at that. She still wasn't acting like herself and he didn't like where this was going. It irritated the hell out of him when she talked like that, as if she had no worth, especially as of late. They really needed to talk, but they never seemed to be alone long enough for him to gather the courage to bring the subject up. It was frustrating him to no end.

"Not so sure about that," he muttered. He sighed. "I just hope I can get through this without falling apart. I'd really rather just quietly pay my respects later when no one else is there."

"We could just turn around right now and go home, or go out somewhere for the day?" she suggested. It was a suggestion she had made before. She was really worried about what this day might do to him.

He shook his head. "I feel obligated to go, I just don't want to be put on display."

"People want to put their heroes on display," she said. "Though the politicians are probably just looking to score points and have a photo op."

"I'm not a hero," he said a bit testily.

"We're not going to have that argument again are we?" she asked.

"Only if you keep bringing it up," he returned.

"I keep bringing it up because it's true." She sighed. "Even your negative reaction to the idea confirms it. A true hero doesn't seek recognition for his heroism. One day I'm going to make you accept this."

"Whatever," he muttered, dismissing the subject. "I just want to get through this and be done with it."

"I still think we should just go to the movies or something," she said.

"If you want to bail out and go to the movies, then go," he groused, his fatigue and irritation over the whole event getting to him. "I'll be fine going on my own."

"I'm not going to bail out on you!" she shot back indignantly. She would never do that to him. "Geez, you've been so touchy for the last month."

"And what about you?" he blurted out, no longer able to contain himself. "You're my best friend and you've been acting like you don't want to be around me anymore. If that's the case then go and do whatever you want. Like you said, I'll be fine without you."

She stopped dead, feeling very much like she had just been punched in the gut. He kept walking. "Shinji! It's not anything like that." Her voice took on a desperate tone. "Shinji…wait!"

He didn't break stride as he walked to the next street corner and turned right, continuing towards the school. She was well aware that for the last month she had been acting differently around him, but she had no idea that he was feeling like she didn't want to be around him. That was the farthest thing from the truth that could ever be said. She was also well aware of what had started all of this and it was her fault.

She massaged her temples with the heels of her hands and let out a long sigh. "Way to go Misato," she admonished herself. "He's the best thing that's happened to you in your entire miserable life and you're screwing it up because you can't get your shit together."

With her mind in turmoil and her eyes cast down to the pavement, she slowly followed after him.

Two blocks further up the street, Touji, Kensuke, Hikari and Asuka waited for their friends to meet them, as they did every morning on the way to school. When they saw Shinji drawing near with Misato better than a block behind him, they knew something was up. It was completely out of character for those two not to be all but joined at the hip. It was pretty rare for one to go anywhere without the other, and especially not during the morning walk to school.

"Yo, Shin-man, what's the deal?" Touji called out to him with his usual lack of tact or subtlety. He still had an undeniable crush on Misato.

"Nothing that concerns you," Shinji muttered irritably as he kept walking, leaving his fellow 'stooges' slack jawed in his wake.

"Go with him!" Hikari hissed at them, somewhat more sensitive to how this day was effecting everyone.

"Wait up Shinji," Kensuke called as he started after him. He was a little quicker on the uptake than Touji who had to hurry to catch up lest he feel the considerable wrath of his girlfriend.

"What a wonderful way to start the day," Asuka groused. "I knew I should have stayed in bed this morning."

"Misato?" Hikari called out as the sad and distracted looking girl drew near. "Are you alright?"

"Hmm…oh, hi…I'll be alright," Misato responded, her mind clearly off somewhere else.

"You and the baka have another spat?" Asuka asked as they resumed walking. Misato nodded. "What about this time?"

"I guess I suggested one too many times that we should skip out today," she answered.

"So he's still going?" Hikari asked.

Misato sighed. "He says he feels obligated to go and I can't talk him out of it."

"He's an idiot," Asuka grumbled. "He's no more ready for this than I am."

"Speaking of which," Misato said. "I thought you weren't going?"

"I'm not," Asuka answered. She held up a plain white envelope. "But the principal won't let me get out of it without a letter from my shrink. _Der Commandant _insisted I deliver it to him in person."

"Do you think he'll be okay?" Hikari asked.

"I don't know," Misato answered.

"If he starts to freak out, get him out of there," Asuka told her, her tone dead serious. "Drag him by the scruff of his scrawny neck if you have to, but don't let him get hurt by this. He's been hurt enough."

It was still strange for Misato to hear Asuka show such concern for Shinji, or anyone else for that matter, but it was a good sign of the way she was changing.

"I will," she promised. "Even if he thinks I don't want to be around him, I won't leave him alone."

"What?" Hikari said, wondering if she had heard correctly.

"Just what exactly did he say to you?" Asuka demanded.

Misato sighed and told them what had happened. She nearly started to cry at the idea that he thought she didn't want to be around him.

"Well what did you expect him to think with the way you've been acting for the past month," Asuka admonished. If nothing else, she could always be counted on to be unapologetically blunt.

"Asuka!" Hikari exclaimed at the redhead's seeming lack of sympathy.

Asuka stopped and looked Misato in the eye. "This all started a month ago after you were sick and missed a week of school, and our beloved baka Shinji went over to your place to help you catch up on all the work you missed. Right?"

Misato could only nod in confirmation.

"I may not have been there," Asuka continued. "But I know the two of you better than anyone else does and I'm pretty sure I know exactly what happened that night."

The fact that Misato could no longer meet her gaze confirmed her suspicions.

"Look," Asuka said, softening her tone somewhat. "You need to take care of this and make things right between the two of you. You and Shinji are two of the most important people in my life and I don't want to see you miserable, we've all had enough of that to last a dozen lifetimes already. You've let this mess go on too long."

"I know," Misato admitted, her eyes becoming moist. "I've been having a lot of trouble lately separating who I was from who I am or who I want to be and it's gotten in the way."

"And you've been acting like I used to by not letting your friends help you," Asuka said. "Don't make the same stupid mistake I did. Once this dumb memorial thing is over the two of you need to find out where you stand with each other. If I've learned anything from my shrink it's that you can't keep the people who care about you at arms length. I doesn't do a damn bit of good."

She turned to resume walking, but stopped and turned back to Misato again. "Oh, and just so you don't think I've gone soft, if you hurt him, or break his heart, I'll rip your lungs out. I did enough damage to him and I don't want to see him hurt anymore."

"I would never hurt him Asuka," Misato vowed, her voice a little shaky. "That's the last thing I would ever want to do to him."

"Do you want to talk about what happened?" Hikari asked, genuine concern in her voice. She had become pretty good friends with Misato after getting over the initial shock of finding out the truth about her. She was willing to do whatever she could to help. Being the kind person she was, she felt so badly for the terrible things her friends had had to go through.

"I don't want to pry, so if you don't want to that's okay," she continued, worrying that she was coming off as sounding nosey.

Misato wasn't sure if she wanted to share what had happened that night. She was ashamed of herself and she was really worried about what they would think of her if she told them. She knew Asuka was right. She needed to talk to Shinji and she had already put it off too long, their tiff earlier confirmed that. She had been so deep in her own self pity that she hadn't seen how her behaviour had been affecting him.

Telling Asuka and Hikari about it might help, but then again it might earn her the scorn she felt that she deserved. If they did react that way, she wasn't sure she could handle it. In the end, their looks of concern and understanding won out and she spent the rest of the walk to school telling them what happened and confirming Asuka's suspicions.

* * *

Shinji's head ached and he felt vaguely dizzy as he sat in his front row seat near the still covered memorial. He clenched his fists in a futile attempt to stop his hands from shaking and wished his stomach would stop trying to turn itself inside out. Even scaring the hell out of one of the event staffers earlier hadn't made him feel any better.

Shortly after arriving a man from the committee who had been hounding him on and off for the last month had come up to him to tell him at what part of the ceremony they would be calling him to the stage. He had reminded the man again of all the times he had already refused to be a part of it, but the guy just gave him a greasy smile and said it was going to happen whether he liked it or not.

'_No, it won't,' _he told the guy, giving him a glare that was part Gendo Ikari, part Unit 01. The guy couldn't get away from him fast enough.

The remainder of the walk to school had passed pretty quietly once Kensuke and Touji realised that he wasn't going to tell them what happened between him and Misato, and the trip to the park had been equally as quiet. Misato had been beside him the whole time, looking even more worn than she had earlier that morning, and he found himself afraid and unable to say anything to her.

As he listened to the Secretary General drone on with his speech, he found himself wishing that he had taken Misato up on her suggestion to just skip the whole thing. Even his therapist had warned him that he should probably stay away, but he thought he could handle it. Maybe he could have if the memorial committee hadn't been pressuring him to be part of the unveiling. It had brought his nightmares out with greater frequency and intensity and he had been having a few flashbacks that he hadn't even told Misato about. He was a wreck, but it wasn't until this moment that he realised just how much of a wreck he really was.

He could almost feel the sense of worry radiating from Misato as she sat to his left and he felt so bad for what he had said to her earlier. They had had little arguments and disagreements before, but neither of them had ever snapped at the other like he had done to her. He knew that she just wanted to help him, but the pressure he felt over the memorial issue and the strain in their own relationship lately had built up within him until he had snapped. He couldn't help but think that his life was starting to drift out of control again.

He was beginning to sweat and it wasn't just due to the heat of the sun as it beat down on him. When the Secretary General began to speak about the bravery and sacrifice of the Eva pilots, his head swam violently and he nearly threw up. His heart was pounding and he was breathing hard, not entirely sure that he wasn't going to pass out.

He wished the man would just shut up, or better yet, turn into a puddle of LCL and dry up under the hot sun. What did he know about what they went through? He was a politician who had sat in his safe little office, thousands of miles away from the conflict, oblivious or uncaring to the fact that SEELE had been using the very organization he was in charge of to fund the ultimate destruction of mankind for their own selfish and deluded purpose.

When he started to talk about the pilots individually, and he heard him speak Rei's name, he knew he had to get out of there. He didn't care if anyone thought he was running away. This man wouldn't know Rei if she suddenly appeared and slapped him across the face. He didn't know any of them or what kind of hell they had gone through and he wasn't qualified to speak to it.

The steel folding chair he had been sitting on clattered loudly against the concrete, knocked aside as he lurched to his feet and took off in a stumbling run. The speech stopped as the Secretary General saw his photo op going down the drain, and a murmur arose in the crowd at the commotion.

With no hesitation Misato was on her feet and following him, straight-arming their protesting school principal out of her way as she ran after the most important person in her life.

* * *

A/N: Wow, it only took me three weeks to finish this chapter. I must be shaking off the rust.

I hope everyone liked this and really do hope you leave a review. I always look forward to them.

Within a day or two I should be started on Chapter 3. I know what I want to do with it, so it's just a matter of hammering it out, but I'm not going to rush it.

Until then, enjoy what's here and while you're hanging about, why not check out my other stories and maybe leave a review there too.

You know how to find them.


	3. Chapter 3

**Disclaimer: **I don't own Neon Genesis Evangelion or anything associated with it. Gainax created this world, I just play in it.

Well, it took longer than I anticipated, (largely due to some personal issues) but here it is, the last chapter.

Please read and review.

**Thirteen**

_**Chapter 3:**_

Misato sat in the shade on a park bench. The cheerful chattering of the birds and the quiet beauty of the well tended park were lost on her as she closely watched Shinji as he stood at a nearby vendor's cart. She had chased him all the way to the other side of the park, not catching him until he had stumbled to a stop next to a water fountain.

He had been doubled over and trying to catch his breath, his hands locked tightly onto the edge of the fountain, when she stopped beside him and tentatively placed her hand on his back to let him know that she was there for him.

He had flinched and pulled away from her like her touch had burned him.

'_Leave me alone!'_ he had wheezed, the catch in his voice making her realize that he was crying. _'Please…just for a few minutes.'_

'_O..okay,'_ she had stuttered rather meekly, before taking up her current position on the bench.

She had begun to cry herself as she watched him there with his head hung low and his shoulders shaking. She had seen him hurt so many times before and she always felt so helpless to do anything for him. She wanted nothing more than to go over there and wrap her arms around him and tell him that everything was alright.

But the truth of the matter was, she didn't know if it would be, or if she even believed it could.

'_We're falling apart,'_ she had lamented. _'I thought we were moving forward and getting stronger. I don't even know if we can lean on each other anymore.'_

It took a long time for him to regain his composure, finally splashing some cool water from the fountain on his face before turning and walking away. She was afraid that he was going to leave her there and was unsure about going after him if he did. Thankfully he had stopped at the vendor's cart.

She sniffled and wiped the remaining dampness from her eyes, wishing that she could just start the whole day all over again. No, actually she wished she could have the last month or so back to do over, but that wasn't going to happen either. If only she hadn't been so wrapped up in her own self pity to notice how it had been hurting Shinji.

"Here," he said to her, his gentle voice cutting through her thoughts. She took the ice cream cone he was holding out to her. Raspberry swirl, one of her favourites. He sat down next to her and began eating his own.

"Vanilla again?" she asked.

He shrugged. "I like vanilla," he said simply.

They remained silent as they ate their ice cream, both trying to order their thoughts. Now would be as good a time as any to try and get things straightened out between them. They both knew that things couldn't continue as they had been.

Shinji finished his cold treat first and finally turned to look at her. Since sitting down he had avoided doing so for two reasons. One was the need to concentrate on his own thoughts and to get things straight in his mind before he spoke, for fear of making a fool of himself.

The second was that watching Misato Katsuragi eat an ice cream cone was an exercise in unintentional eroticism that he didn't need to see right now. He definitely didn't need to have the blood leave his head for the southern regions of his body at this point in time.

"I'm sorry," he began softly with his usual refrain. "About earlier and for this morning. I shouldn't have snapped at you like that."

"Well, I was being a bit of a pain I guess," she said, trying to absorb some of the blame he felt.

"No," he said with a shake of his head. "You were trying to look out for me like you always do and I threw it back in your face." He sighed. "You were right, we should have skipped out. We should be in a movie theatre right now watching a bad movie and eating bad popcorn."

"So…do you really think that I don't want to be around you?" she asked, really afraid of what the answer would be.

"I don't know," he answered quietly, ashamed that he couldn't say no. "You used to glomp me every morning and try to get me to give you a piggy back ride to school. You used to goof around and spontaneously hug me or grab my arm when we were walking and when we were joking around with our friends. You used to tease me just like you always did. But now you don't glomp me or grab me and you barely tease me at all. I don't know what to think now." He paused for a moment. When he resumed speaking it was in very quiet, sad voice.

"That night at your apartment…I was such a coward and I know I really hurt your feelings. I guess I really can't blame you if you don't want to be around me."

'_What have I done to him?' _she thought frantically. Not only did she have him thinking she didn't want to be around him, but he was blaming himself for it.

"But you didn't do anything wrong," she cried, unable to stop the tears from coming again. "It's all my fault Shinji. I'm the one who messed up and I should have known better. Damn it, I did know better but I couldn't stop myself. I'm the coward, I'm the one who hurt you and instead of apologizing I kept my distance."

"But I couldn't give you what you wanted Misato," he said, his subconscious and almost pathological habit of taking the blame rising to the surface. "And I ran away like always."

"Don't you dare," she sobbed. "Don't you dare take the blame for this. You're the victim. I tried to use you just like I always used to because I'm stupid and I'm weak and I don't even know who I am anymore."

"You're not stupid and weak Misato," he countered. He was starting to tear up again himself, seeing her like this.

"Yes I am Shinji," she sobbed. "And because I am I did something inexcusable. I know you. I know what makes you happy and what scares you and what I tried to do is right near the top of your list of fears. I knew it, but I did it anyway. What kind of friend am I Shinji that I could do that to you?"

_**

* * *

**__**One Month Ago**_

"Finally," Misato sighed with satisfaction. "Thanks a lot Shinji, I don't think I could have gotten all this done without you." She cemented her thanks by leaning into him and kissing him on the cheek.

"N..no problem," he stuttered.

Sure enough, it had been a strange and nervous evening for him. She had been sick for most of the last week, though she could have gone to school today, she had decided that going for one day out of the whole week was kind of pointless. Besides, the flu bug had hit her pretty hard and she needed the rest.

He had brought all of her homework assignments with him when he got home from school, using them as ammunition to get past the guard dog that was Misato's building manager. Mrs. Ajibana didn't really like having the boys and girls from the residences she and her husband managed going to each other's apartments. She was positive they would be up to no good, but she did trust a few of them more than others and Shinji happened to be on her good list. Having the armload of homework assignments was a bonus that helped get him through the door.

He should have known something was up when Misato, wearing a black t-shirt and blue jeans, both of which clung tightly to her eye catching curves, greeted him with a longer and tighter than usual bear hug. She was also wearing a little bit of make up and the slightest hint of familiar lavender perfume, something she rarely did. While it was true that the only contact they had had for the week was a nightly chat on the phone, by the way she was acting you would think they hadn't seen each other for months.

He was used to a certain amount of physical contact from Misato. It came with the territory and it had taken him a long time to stop flinching and stammering like a fool whenever she glomped him, but there was something different about this. As he went over the assignments she had missed and then started dinner for them, she remained very close to him, almost in constant contact. When they were sitting on the couch she was close enough that their legs touched and neither of them could move without brushing arms or shoulders together.

As she was helping him cook dinner she seemed to always be lightly brushing her body against his as they moved around the small kitchen. He lost count of the number of times their hands touched or her hip would bump his as they worked at the counter, and he kept catching her looking at him and he couldn't quite identify the look in her eyes, but it made him nervous.

It was more of the same when they finished eating and did the dishes, and when they sat down on the couch to resume doing her homework. Even when he tried to put a little bit of space between them, it would soon disappear.

He had never been good with physical contact with anyone and especially not with a member of the opposite sex. Even after all of the bear hugs and playful headlocks he got from adult Misato, and all of the similar contact from her younger self over the past two years, the problem still remained.

His fear of contact wasn't rooted in the physical, but in the emotional part of his life. Losing his mother, being abandoned by his father, being treated with disdain by the teacher his father left him with, all of these things served to build a shield around him that he used to hide from all things painful and unpleasant. It stripped away any sense of self esteem he may have had and convinced him that he was a loathsome, useless person, unworthy of any kind of positive interaction with others. Every negative thing that happened to him only reinforced it in his mind.

Isolating himself meant no contact and no contact meant no pain, be it physical or otherwise. If you had no contact or connection with someone, no matter how much you wanted to, it didn't hurt when they left you. Mix in the usual nervousness of a very shy teenaged boy being around a very outgoing and beautiful teenaged girl and you had a recipe for disaster.

He could only describe her actions as being somewhat…amorous. The physical contact, the way she looked at him, the way she smiled at him, the way she spoke and the tone in her voice had him torn in two directions.

One side of him was enjoying it and was exhilarated by it. It was an absolute truth, one which he hadn't shared with anyone, that he was in love with Misato. That realisation had finally cemented itself in his mind over the last few months. She was beautiful, she was a lot of fun to hang around with, and they knew and understood each other so well. They were always there for each other no matter what, and he felt that she was largely responsible for the slow but steady progress he was making in his life.

The way she was acting tonight had definitely gotten his attention.

The other side of him however, was beating the snot out of the side of him that was enjoying the attention. Quite frankly, he was scared to death. She was being seriously flirtatious and the little touches, and especially that kiss on the cheek, were sending panic alarms ringing in his head. Being playfully glomped and hugged were one thing, but this was a whole different animal. This was serious business.

And it was only getting more serious by the minute.

She wrapped her arms around him, holding him tightly to her oh so warm and soft body. "I've been pretty lonely around here all week by myself Shinji. I missed hanging out with you."

"M..me too," he said. He was having trouble thinking. How could something that felt so nice, be so scary at the same time.

She giggled. "You're so cute when you blush like that." She kissed his earlobe, making him shiver. What she said next nearly gave him a stroke. " Do you wanna fool around a little Shinji?"

"Wha..what?" he squeaked.

The next thing he knew he was on his back on the couch with Misato laying on top of him. Her soft lips were on his and her right hand was gliding through his hair. He went rigid, paralyzed with both fear and wonderment. The part of him that loved her wanted to go with it and return the kiss, but again the other side won out.

"M..Misato," he gasped, finally able to move and break the kiss.

"Relax Shinji," she whispered in his ear, cutting him off before he could say more. She kissed her way down his neck and started to unbutton his shirt with her left hand. "I'm not going to hurt you."

Her warm breath tickled his ear, sending a shiver down his spine. The feel of her lips on his neck and her hand stroking his chest inside his shirt was highly distracting and would have felt damn good if he wasn't on the verge of a panic attack. Again, that one part of him wanted what she was doing and wanted to give her whatever she wanted, but the other part was in control.

"I.. I… d..don't think we should do this," he stuttered. Unfortunately, a certain part of his anatomy was having other thoughts and reacted in the same way it seemed to do so very often around her. And like usual, she did not fail to notice.

"It's not so bad is it?" she whispered in his ear again before giving it a playful nip. "One part of you is interested it seems. Just go with it Shinji, you'll like it."

He felt almost claustrophobic and he was sure he was going to hyperventilate. His stomach was twisted into knots and his heart was pounding. He was in full panic mode. He tried to squirm out from under her, but couldn't. Even now she was still stronger than he was, and she didn't want to let him go anyway.

"P..please Misato, s..stop it!" he stammered, almost in tears now. "I..I can't. P..please!"

His plea, if it was heard, was ignored. He felt trapped and was becoming frantic. He was also ashamed of himself. Any other boy in his position would have been overjoyed at the attention he was receiving, but not him. Once again he was Shinji the coward, Shinji the wimp. He continued to plead for her to stop, his stammering and stuttering practically incoherent. He couldn't even manage a simple, forceful 'NO'.

Her mouth was on his again, silencing his ineffectual protests. She kissed him with a ferocity that made him think she was trying to devour him. Her body felt so hot against his. As her hand was fumbling with his belt, his panic went full tilt.

With a surge of adrenaline he managed to roughly roll her off of him. They fell off the couch and knocked the coffee table over, sending school papers flying. He scrambled to his feet and quickly gathered his book bag and his shoes.

"I-I-I'm sorry," he wheezed, tears running down his face. "I ha-have to go." He practically fell out the door and into the hallway as he made a hasty, stumbling exit.

Misato sat on the floor staring at the door. She was trembling and tears were rolling down her face. She felt as if she had just awakened from a trance and the full realization of what she had been doing had just hit her like a hard slap in the face. She knew Shinji better than anyone and she knew that he had issues with human contact, intimate or otherwise. He had been like that from the time she first met him and it was still one of the biggest issues in his life, even though he and his therapist had been trying to fix it.

And she had just tried to force herself on him. The look on his face as he left was burned into her mind.

He had been terrified.

"Oh god," she sobbed. "What have I done?"

_**

* * *

The Present**_

"Why did you do it?" he asked softly.

"Because I still seem to equate love with sex and I was feeling lonely," she answered, wiping tears from her face with a trembling hand. "I was alone that whole week and when I'm by myself for very long I get lonely and start thinking too much about the past. I've always been lonely and it doesn't take much to make me feel that way and I lose myself to it." She managed a little smile. "The only time I don't feel lonely is when you and I are hanging around together."

"I like hanging around with you too," he said. "I always have. That's one reason why this last month has been so hard, because it was like you weren't even here."

She couldn't look at him, as ashamed as she was at how she had acted. "My loneliness was why I used to run off to see Kaji, you know. I wanted someone to love me so that I wouldn't feel lonely anymore and even though he never told me that he loved me, I still kept going back to him. I knew it was bullshit, but somehow I convinced myself that letting him screw my brains out was an act of love and for that short time, I wasn't lonely."

She shook her head sadly, her eyes downcast. "I was so stupid. The week I was sick I fell back into that way of thinking. It was pretty easy really, since from one day to the next I don't really know if I'm the adult I used to be or the girl you see in front of you right now. I was confused and lonely and wanted to feel loved and I fell right back to being that filthy thing I used to be."

"And I couldn't give you what you needed," Shinji said sullenly, unable to look at her.

"And I'm glad you didn't," she said softly, finally able to look at him again. "What I did was bad enough, but if I had gotten my way it would have been worse. I was using you for my own selfish and stupid reasons, just like I did for my revenge against the Angels. The worst part of it was that I knew you would get scared just like you did, but I did it anyway. I'm still a rotten, worthless human being, just like I was then and I don't even know how to go about asking for your forgiveness. I know I don't deserve it."

"Stop running yourself down!" he snapped, his usual frustration at her self degradation rising to the surface. "You're not rotten and you're not worthless!"

"I'll stop when you do!" she countered. "And when you stop blaming yourself for things that aren't your fault!"

They glared hard at each other for a moment, brown eyes challenging blue, before finally he closed his eyes and sighed.

"I guess neither of us has our act together as well as we thought we did," he stated quietly.

"I guess not," she agreed.

"I really wanted to talk to you the next day," he continued. "But I couldn't make myself walk out the door and I spent half the day picking up the phone and putting it down again without dialling."

"I probably wouldn't have answered," she admitted. "I spent the night on the floor where we landed when we fell off the couch and most of the next day locked in my bedroom in the dark, crying about what an idiot I was. I was afraid that you would hate me."

"I would never hate you Misato," he assured her. "We're both idiots because we let it drag on. Even after all of the time we've spent talking about the things we both did or didn't do in our lives and why, we let this go on." He sighed. "I didn't know what to say or how to go about fixing this."

She began to unconsciously fiddle with the hem of her skirt. "I kept my distance because of what I did, and I realized that I had already been taking a lot of liberties with you all along, by always mauling you like I was. I'm so sorry Shinji, I shouldn't have been doing that."

"I didn't mind," he said sheepishly.

"You didn't?" she questioned, a little confused. "But you usually get nervous and embarrassed. Your face turns red, and you start stuttering."

He shrugged. "But I'm not as bad as I used to be. And you always seemed so happy. It makes you laugh and smile so I don't mind. It became normal and I actually missed it when you stopped. Teasing and glomping me has always been how you've shown me that you cared about me and I was afraid that I had lost that."

"Shinji…" she was nearly speechless. "I really do care about you. I always have." She took a deep breath to steady herself. "I guess in my own, strange and twisted way, that was part of what happened that night. I wouldn't have tried to do that with just anyone, despite my past reputation."

"I know," he said softly.

She had told him during their many talks that despite the way she projected herself to the world, she really wasn't the promiscuous woman that everyone thought she was. Kaji was the only man she had ever been with.

He had liked Kaji, but it bothered him that he had been so willing to help her dirty herself and that he had never once told her that he loved her. It made him wonder if Kaji really did or not. But she had loved him and it was the only way she had known to try and escape her crushing loneliness.

'_Wait a minute,'_ he thought as his brain put two and two together. "Does that mean…"

"Yes," she cut in, shakily, doing her best to make her eyes meet his hopeful gaze. "I love you Shinji, I really do and I'm so sorry for what I did. I messed up really, really bad and then I didn't know how to undo it and I made it worse." She sniffled and rubbed the tears from her cheeks. "It hurt a lot to keep my distance and I want to be around you like I used to be. Can you ever forgive me Shinji?"

'_She…she loves me…?' _He wasn't sure if he dared believe it and he was both hopeful and afraid at the same time. There was no doubt that he loved her, and there was also no doubt that he had been hoping that she felt that same way about him. But old, deep rooted fears did not wane easily and they made one think in strange ways. He had actually been afraid that he would lose that love before he ever even knew that he had it.

He looked into her beautiful brown eyes, seeing the desperate hope in them, the hope of a sad and lonely soul that just wanted to be loved. He noted the tears trailing down her cheeks. God how he hated to see her cry. That face was not one that should be stained with tears of sadness and pain. It was supposed to be laughing and smiling and filled with mischief.

'_Hurry up and say something you idiot,'_ he admonished himself. '_Before she gets the wrong idea.'_

"I forgive you Misato," he said, happy to see the relief on her face. "And…I," he swallowed hard. "I love you too."

Her eyes widened a bit. She had been afraid that he wouldn't feel the same. "You do? Even after what I did?"

He nodded. "I've been trying to find the courage and the words to tell you for a while now. I'd get myself talked into telling you and then I'd chicken out." He frowned. "I was also afraid that if you didn't feel the same way that I would have ruined our friendship…I don't think I could take that."

"Our friendship won't change Shinji," she assured him. "We died together, got a second chance together, and have held each other up through good and bad. That's pretty strong."

"I was determined that I was going to tell you that night when I came to your apartment," he admitted sheepishly, nervously scratching the back of his head. "Then I spent ten minutes staring at your door like an idiot before I finally rang the bell and I wimped out again."

A wave of fresh tears began to stream down her face, but this time she was smiling.

"Misato?" he asked, a little puzzled.

"Can…can you say it again Shinji? Please?"

He smiled and nodded. "I love you Misato." There was more confidence in his voice this time.

"I've wanted to hear someone say that for so long. I'm glad it was you Shinji." She seemed genuinely happy, more like her usual self.

Without thinking, she suddenly lunged at him and wrapped her arms around him. For a moment she was stricken by the fear that she had just messed up again because his body tensed. She was about to pull away, ashamed that she didn't seem to be able to control herself, when she felt his arms tentatively go around her and then he gently embraced her.

"Thank you Shinji," she said with a catch in her voice as she relaxed into him. "And I promise I'll never try to use you like that again."

"There was a part of me that wanted it," he said, sounding ashamed of himself. "And that scared me even more than I already was. I…I'm just not ready for something like that."

She pulled back from him a little so she could look into his eyes. "I know, I knew that then I think, and I'm so ashamed of myself. I..."

"It's okay Misato," he cut her off, smiling. "We can forget that night and start fresh right now can't we?" he asked hopefully.

She returned the smile. "Yeah, Shinji. We can."

They found themselves staring into each other's eyes, both feeling greatly relieved. It was then that Shinji did something distinctly un-Shinji like. He took the initiative and he kissed her.

He didn't really know what made him take such a bold move, he just simply did it without thinking about it. It wasn't much, just a quick, soft peck on the lips, but it sent a tingle down his spine nonetheless.

By the look on her face it was obvious that he had surprised her, and he suddenly got the feeling that he had made a mistake. He was about to apologize for his grievous error when she smiled and kissed him back before the words could make the short journey from his brain to his mouth.

A year ago, he couldn't have seen this happening. Despite her appearance, in his mind she had still been the grown woman who had been his guardian and commanding officer. But as she had begun to act more and more like a teenager, his perception slowly began to change. Six months ago he realized that he was beginning to have feelings for her that were beyond mere friendship and it wasn't long before he came to the realisation that he was seriously in love with her.

As she broke the kiss and held him tightly to her, she felt like a great weight had been lifted from her. The boy she loved had not only forgiven her, but had told her that he loved her. She had been so unsure of who she was that she hadn't been able to tell him before.

In her old life she had found herself having some rather inappropriate thoughts about her young charge at times, adding it to the list of things she tried to drown with beer. Regardless of that, and as sappy as it sounded, he was her hero, and he had been from the moment he climbed into Unit 01 for the first time.

In this new life, she trusted him like she hadn't trusted anyone else before. He had never tried to take advantage of her, even though he could have after she woke up on the beach, since she had been too weak to defend herself. He could have done anything to her and she wouldn't have been able to stop him.

Many would have, but Shinji kept on being Shinji. He helped her, looked after her, even fought to protect her. He treated her with dignity and respect, never once trying to cop a feel like so many of the other boys at school had. Even when she caught him looking at her it was just a quick glance because he didn't want to offend her by staring.

New life or old, through good times and bad, he had stuck by her. Sure enough, they still had problems to deal with and it would take time and tears to do so. But now that they had said those three words to each other, she felt more confident than ever that they would be okay.

She pulled back from him again and smiled. "Thank you Shinji."

"For what?" he asked.

"For just being you. For everything you've done for me."

"You've done a lot for me too Misato," he said. "You've always tried to help me live and be better. You've always tried to be there for me no matter what I did. It doesn't seem like enough, but thank you."

"So I guess you and I are good again huh?" she teased.

He laughed. "Yeah, I'd say so. So, do you still want to go to the movies?"

"Good idea," she said as she stood up and wiped away the last of her tears. "We can make our escape before the principal catches up to us. I kind of knocked him on his butt when I ran after you."

"I know where we'll both be tomorrow then," he groused, not anticipating a trip to the principal's office.

"You worry too much," she laughed as she grabbed his hand and pulled him along. "Let's go, I think the theatre is having a Godzilla marathon."

"We're going to watch movies about giant monsters?" he asked disbelievingly.

"I know, I know," she conceded. "But I like Godzilla and you don't want to disappoint your girlfriend do you?"

'_My girlfriend…?'_ he thought, a little dumbstruck, as she led him along. _'I like the sound of that.'_

_**

* * *

Two Weeks Later:**_

"Look's like it will be a beautiful day," Shinji said to himself as he leaned on the railing of his apartment balcony, regarding the clear blue sky before him. It would be a good day for the trip to the beach with Misato and their friends.

Unlike two weeks ago, he was well rested. The nightmares had pretty much stopped, he had only had one in the last fourteen days, and he was much happier than he had been even before the problems with Misato and the memorial dedication had come up. And with the next week off from school, he could relax and have a little fun.

Of course, having a relationship with someone as fun to be with as Misato, he couldn't help but be happy, and being her boyfriend had only added to his good mood as of late. Telling each other how they felt had removed an invisible barrier that neither of them had known was there, and had opened up a new wave of emotions for them.

For them both, knowing that someone truly loved them was helping them to lose the long held fear of letting someone get close to them and they were feeling more confident about themselves by the day. They found themselves able to express their feelings to one another without the self doubts and angst that had plagued them both for so much of their lives. Together they had lost the notion that they were unworthy of being loved.

Of course, there were other positive and enjoyable things about their new relationship too. He had discovered, after much initial nervousness on his part, that he really liked kissing Misato.

He really, really, liked it.

Movement across the way caught his attention as Misato slid aside the curtains and opened her balcony door. He smiled as she groggily stepped out into the warm morning sun, one hand covering a yawn, the other ruffling through her dishevelled purple hair. Past or present, alcohol or not, she was always a wreck first thing in the morning.

As she stretched her arms above her head and arched up onto her toes, he drank in the sight of his beautiful girlfriend with a happy little sigh. Recently his late awakening hormones had prompted him to start noticing her in a little different light. She was no longer just Misato, his best friend and the girl who kept raiding his freshly done laundry for her sleepwear.

He had begun to really notice the curves and contours of the beautiful girl who owned his heart. He had begun to notice things like the shape of her legs and the gentle swell of her slim hips. The unblemished skin of her flat stomach and the way the short grey shirt she wore to bed clung to her generous breasts, especially as it rose up her body as she stretched, barely keeping those bountiful assets contained.

He heard her laughing and realized that he had zoned out and had been caught staring. He would definitely get teased about this for the rest of the day. Though, he couldn't say that he really minded.

He returned the wave she sent his way and watched her saunter back into the apartment, purposely swaying her hips as she went.

God, but she had a cute butt!

He heard a sudden, short shriek and started to laugh. Apparently PenPen had struck again.

"That penguin has way too much fun at her expense," he said with a grin. Hearing the tea kettle beginning to whistle, he went inside for breakfast.

* * *

"I'm late again!" Misato groaned as she worked a pair of faded denim cut offs up over her hips. "Of course I wouldn't be if I hadn't had to chase down a certain penguin because he ran off with my bikini top!"

A nonchalant 'Wark' was heard from the direction of the couch were said penguin was reading the paper.

'_He's faster than he looks, I'll give him that,'_ she thought as she put on the now retrieved top and covered it with a dark blue tank top. "You know, I could be nasty and cut off your internet access so you can't trade stocks or play poker with your online friends," she threatened.

"Wark?" PenPen squawked fearfully, the paper shaking in his flippers.

"But since I love you, I'm inclined to forgive you."

PenPen warked a sigh of relief. He had an extensive portfolio to manage and being cut off from the net for any period of time would be disastrous. That and there were pigeons to be plucked for his amusement in the poker rooms.

Misato rummaged through a small backpack to ensure that everything she had packed into it the night before was still there. A change of clothes, her beach towel, a bottle of tanning lotion, and all of the other various items she had packed were still there. Satisfied that she had everything, she went to the door and put on her shoes.

"Behave yourself while I'm gone PenPen," she said. "If you're really good maybe I'll ask Shinji to do up some more of those fish like he brought you last week."

PenPen dropped his newspaper and turned to face her, his right flipper raised to his head in a stiff salute.

"Wark!, Wark Wark!"

She could almost see the little hearts in his eyes. He had _really_ liked those fish.

"Smart ass," she muttered, rolling her eyes as she went out the door.

She rushed down the stairs and out the building's front door. Sure enough, and like usual, Shinji was there waiting for her. He was dressed in a pair of dark blue beach shorts and a blue and green tropical print shirt that she had bought for him, because she thought he would look good in it.

And he did.

She had been feeling a lot better about herself over the last couple of weeks, and it was all due to the unassuming young man standing before her.

He loved her. He really and truly loved her. She could hear it in his voice and see it in his eyes whenever he looked at her. It gave her a feeling like she had never known before in her life. She felt wanted. Not for her looks and her body or her military abilities, but just because she was herself.

She was no longer twenty nine year old Major Misato Katsuragi, Operations Director of NERV, drunken sex toy to Ryoji Kaji, and the dirty woman everyone loved to gossip about when they thought she couldn't hear them.

She was sixteen year old Misato Katsuragi, student at Tokyo-2 Central High School and girlfriend to the shy and cute Shinji Ikari.

She was also very happy.

She rushed over to him, dropping her backpack next to his, and administered his morning glomping, practically jumping on his back while wrapping her arms around him from behind.

"Shinjiiiiiii!" she cried out happily, drawing dirty looks from the handful of other students who were around that just could not comprehend why 'such a hot babe like her was going out with Ikari'.

Shinji stumbled a bit but kept his balance, as used to Misato's affectionate tackles as he was. "Good morning Misato," he chuckled.

She kissed his cheek then let go of him. "So, did you see something you liked this morning?" she teased.

His face turned red. "I saw a very pretty girl stretching in the morning sun," he said sheepishly. Flirting required a little more self confidence than he yet possessed. But he was getting there.

She rewarded him with a quick peck on the lips that only made him blush more. They both picked up their backpacks and started on their way.

"We've come a long way haven't we?" she asked.

He nodded. "I never would have thought that my life would be like it is now, with or without Instrumentality. That day, I thought that the best it would ever get would be taking your hand and walking into the end of the world with you."

"And now," she began as she grabbed his right hand in her left and intertwined their fingers. "We're walking hand in hand in a new world where we're both happy and can live the way we want to."

"And instead of fighting giant monsters, we can go to the beach with our friends," he added with a smile.

"And I can watch your eyes pop out when I strip down to my bikini," she teased.

Just the thought of it was almost enough to make his eyes pop out now. Even if she was right, he still thought he should defend himself.

"At least I'm not like Touji, he'll be drooling and his tongue will be dragging in the sand."

"Which will earn him a beating from both Hikari and Asuka," she added with a laugh. "All while Kensuke kills himself laughing trying to film it."

The visual ran through his head and he couldn't help but laugh.

"I love to hear you laugh Shinji," she told him. "And I love to see you smile."

"I have reason to now," he said as he stopped and shyly looked into her beautiful, brown eyes. "I have someone with me who I know really cares about me."

She placed her hand on his cheek. "I've always cared about you Shinji."

"I know," he said. "But I couldn't see it then. All I could see was my own pain and I was drowning in it. You did your best for me and you believed in me when I thought I was worthless and that no one could possibly care about me."

"You did the same for me Shinji. I sent you out to fight, I got drunk and made a mess and made a fool of myself, yet you stuck with me. You stuck with me right to the end and beyond and you gave the world a second chance." She gave him a tender, loving smile. "You gave us a chance, and here we are."

"Living a completely average, normal life," he added.

"It's nice, isn't it?" She gave his hand a squeeze and they resumed walking, off to meet their friends for a day of fun.

Not looking back, but going forwards.

* * *

A/N: I sort of lost the feel for this along the way and it took a while to get it back. Hopefully I didn't completely screw it up.

I hope you enjoyed it and I hope you take the time to leave a review.

While you're hanging around, why not check out my other stories. You know where to find them.


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